I think I've discovered a bug in the OS X driver.
I first noticed this behavior when working with the SDL game development library, but I thought it was related to a patch that was submitted to SDL. I've since begun working with another library, VRPN, where this same behavior is evident.
The behavior is as follows:
When working on a plugin for Cinema 4D designed to allow HID devices to be used for realtime animation/recording I noticed that my Space Navigator wouldn't produce input when c4d was the active window. Only if I had the 3DConnexion driver open in system preferences would the inputs show up in c4d. I even uninstalled the spacemouse plugin in c4d to make sure it wasn't a conflict with that. I wrote it off as a problem with the incomplete 3DConnexion support in SDL.
However, when working on "fixing" this by using another library, VRPN, I noticed this same behavior, except the 3DConnexion driver window didn't need to be open for inputs to register. Instead, I only needed to click away from the c4d window for inputs to register. On a whim I decided to uninstall the 3DConnexion driver (1.6.1). When I did the problem went away and my Space Navigator produced inputs within my plugin in c4d without issue.
So, basically, there seems to be a conflict between c4d and the 3DConnexion driver; regardless of whether the c4d spacemouse plugin is installed or not. It seems more likely to me that the problem lies in the driver, so I'm bringing it to your attention:)
You can see this behavior by using a free version of my plugin (Control4D) that can be found on my site: www.kvbarnum.com/Downloads.html (works with c4d R10+). SDL only supports 3DConnexion devices on mac (I know, odd right lol). I don't know of any other plugins that support 3DConnexion devices in c4d (other than the spacemouse plugin, but I doubt Maxon is going to release the source code on that).